From some spot-checking, it looks like it's minority usage, but not too rare.

Looking at the top 10 or so stories that come up with https://www.google.com/search?hl=en&gl=us&tbm=nws&authuser=0... I see a few that use it in the positive sense: "Being Santa: a perfect storm of fun", "What the perfect storm of cloud, Big Data and the Internet of Things...", "A perfect storm has been brewing for palladium this month which has pushed the metal impressively north-bound..."

The Wikipedia's page on it has an interesting origin[1]:

    The Oxford English Dictionary has published references going
    back to 1718 for “perfect storm,” though the earliest citations
    use the phrase positively, as in a “perfect storm” of applause.

It also notes that the phrase,

    is nearly synonymous with "worst-case scenario," although the
    latter carries more of a hypothetical connotation.

The phrase is relatively rare in normal British English usage, and it's usually used in the ``worst-case scenario'' sense. To me, the word `storm' brings with it a negative connotation, but I suppose it's logical enough, albeit a little strange, that it could be used to describe a positive set of circumstances.

[1]: http://en.wikipedia.org/wiki/Perfect_storm

Is there a term for this kind of thing - where a word or phrase ends up being used in a way that is almost the exact opposite of how it started? ["meritocracy" is another example]

Words that can mean one thing and also the opposite thing are called auto-antonyms or contronyms.

http://en.wikipedia.org/wiki/Auto-antonym

"Cleave" is a great example: http://dictionary.reference.com/browse/cleave?s=t

"Outstanding" is a good one as well

e.g. The outstanding areas of a research project

Agreed, looks like Wikipedia also agrees:

http://en.wikipedia.org/wiki/Perfect_storm

I agree, I also read the headline in a way that something terrible is going to happen to OSS vendors ...